For example, binlog_format is STATEMENT by default. So, if it is not set in my.cnf, it doesn't fail, only when it is explicitly set it fails.

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sudo /pxc/bin/mysqld --defaults-file=/pxc/etc/my.cnf.local --basedir=/pxc --user=mysql --wsrep-cluster-address="gcomm://?pc.ignore_sb=true" --wsrep-start-position='5805bbc4-3038-11e3-937d-aa946afe7370:100' --binlog_format=MIXED
131022 19:29:24 [Warning] WSREP: wsrep_sst_receive_address is set to '127.0.0.1:4001' which makes it impossible for another host to reach this one. Please set it to the address which this node can be connected at by other cluster members.
131022 19:29:24 [ERROR] WSREP: Only binlog_format = 'ROW' is currently supported. Configured value: 'MIXED'. Please adjust your configuration.
131022 19:29:24 [ERROR] Aborting
======================

So, it needs to be either fixed to check for default values or the default have to be adjusted appropriately. Latter is simpler but may break compatibility with mysql.

The " "autoinc_lock_mode" (1) => 2" has been added but wsrep logic prevents it when parallel threads are there. Hence, this change has not been noted in documentation (so you still need to provide in my.cnf). This will be dealt with in a separate issue.